Exploring biological electron transfer pathway dynamics with the Pathways plugin for VMD.

Journal Article (Journal Article)

We describe the new Pathways plugin for the molecular visualization program visual molecular dynamics. The plugin identifies and visualizes tunneling pathways and pathway families in biomolecules, and calculates relative electronic couplings. The plugin includes unique features to estimate the importance of individual atoms for mediating the coupling, to analyze the coupling sensitivity to thermal motion, and to visualize pathway fluctuations. The Pathways plugin is open source software distributed under the terms of the GNU's Not Unix (GNU) public license.

Full Text

Duke Authors

Cited Authors

  • Balabin, IA; Hu, X; Beratan, DN

Published Date

  • March 2012

Published In

Volume / Issue

  • 33 / 8

Start / End Page

  • 906 - 910

PubMed ID

  • 22298319

Pubmed Central ID

  • PMC3288650

Electronic International Standard Serial Number (EISSN)

  • 1096-987X

International Standard Serial Number (ISSN)

  • 0192-8651

Digital Object Identifier (DOI)

  • 10.1002/jcc.22927


  • eng